GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Acidovorax sp. GW101-3H11

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1936
          Length = 272

 Score =  197 bits (500), Expect = 2e-55
 Identities = 109/236 (46%), Positives = 150/236 (63%), Gaps = 4/236 (1%)

Query: 10  PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69
           PLL ++NV + Y   +  ++GV+ +V  GE+  V+G NGAGK+T+ KTI G++ P  G I
Sbjct: 19  PLLRLQNVESAY-GPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRKGSI 77

Query: 70  TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD--KIF 127
            F+G++I       IVR G+ +VP+   VFP LSV +NL MGA+ R D     +D   +F
Sbjct: 78  EFQGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVF 137

Query: 128 AMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVK 187
             FP L +R  Q AG LSGG++QMLA+ +ALM  P L++LDEPS  LSP L  ++FE V 
Sbjct: 138 GYFPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVV 197

Query: 188 QINQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
           +IN+E GT I+LVEQNA  AL  +D GYVLE+GR  +    + L     + E YLG
Sbjct: 198 RINRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYLG 253


Lambda     K      H
   0.317    0.136    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 197
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 247
Length of database: 272
Length adjustment: 24
Effective length of query: 223
Effective length of database: 248
Effective search space:    55304
Effective search space used:    55304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory